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| Status |
Public on Jul 04, 2024 |
| Title |
skin construct, physio, 48 hours, DC1_2 |
| Sample type |
SRA |
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| Source name |
HFF-1, HaCaT
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HFF-1, HaCaT
cell type: immortalized human fibroblasts, immortalized human keratinocytes
group: physio
time point: 48 hours
treatment: DC1
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| Treatment protocol |
After 14 days, half of the constructs were perfused with TNF-α to mimic an inflammatory state. Electrostimulation is tested on normal and inflamed samples, to have unstimulated and stimulated samples, at 1 and 5V in direct current (DC), and in alternate current, at 10 and 100 Hz. Each condition was tested in three replicates, and sampling was done at three timepoints (baseline, 1 h and 48 h) following stimulation.
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| Growth protocol |
Fibroblasts and keratinocytes were cocultured in a collagen matrix for 14 days, until the fibroblasts were embedded in the collagen matrix, and the keratinocytes over them
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Quick-DNA/RNA™ Microprep Plus Kit from Zymo Research and store at -80°C
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Jan 31, 2024 |
| Last update date |
Jul 04, 2024 |
| Contact name |
Christine Nardini |
| E-mail(s) |
christine.nardini.rsrc@gmail.com
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| Organization name |
PICB
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| Street address |
Via dei Taurini 9
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| City |
Rome |
| ZIP/Postal code |
00186 |
| Country |
Italy |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE254696 |
Differential Anti-Inflammatory Effects of Electrostimulation in a Standardized Setting |
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| Relations |
| BioSample |
SAMN39646202 |
| SRA |
SRX23460536 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8048962_13_S12.bamReadsPerGene.out.tab.gz |
372.0 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
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